G'day Mike,
you might try not using the MIDI mapper... NWC will quite happily address your MIDI synth directly
without using the MIDI mapper.
This is, of course, a work around for your underlying problem, but on the other hand, I
never use the mapper anyhow. As for the "disappearing MIDI", are you installing or using any software that may try to override the MIDI configuration?
Can you repair it from control panel without a (I assume) system restore?
Have you checked for spyware and other exploits?
I highly recommend you check the M$ support site
http://support.microsoft.com and search the knowledgebase for similar problems.
...That's probably enough for now :)
Lawrie